Abstract: The present invention describes novel methods for making a substrate for selective cell patterning, and the substrates themselves, wherein the method comprises contacting reactive hydroxyl groups on the surface of a substrate with a hydroxyl-reactive bifunctional molecule to form a monolayer, and using stencils to deposit cell repulsive or cell adhesive moieties in controlled locations on the cell culture substrate. Methods comprising selective differentiation of stem cells to create tissue specific and organ-specific cell substrates, as well as the cell substrates themselves are also provided.